source oldff/leaprc.ff14SB
source leaprc.gaff
addAtomTypes {
        { "M1"  "Fe" "sp3" }
        { "Y1"  "S" "sp3" }
        { "Y2"  "N" "sp3" }
        { "Y3"  "N" "sp3" }
        { "Y4"  "N" "sp3" }
        { "Y5"  "N" "sp3" }
}
CM1 = loadmol2 CM1.mol2
HM1 = loadmol2 HM1.mol2
FE1 = loadmol2 FE1.mol2
1PE = loadmol2 1PE.mol2
EDO = loadmol2 EDO.mol2
loadamberparams HEM.frcmod
loadamberparams 1PE.frcmod
loadamberparams EDO.frcmod
loadamberparams frcmod.ions1lm_126_tip3p
loadamberparams 4ZF6_mcpbpy.frcmod
mol = loadpdb 4ZF6_mcpbpy.pdb
bond mol.400.SG mol.462.FE
bond mol.461.NA mol.462.FE
bond mol.461.NB mol.462.FE
bond mol.461.NC mol.462.FE
bond mol.461.ND mol.462.FE
bond mol.399.C mol.400.N
bond mol.400.C mol.401.N
savepdb mol 4ZF6_dry.pdb
saveamberparm mol 4ZF6_dry.prmtop 4ZF6_dry.inpcrd
solvatebox mol TIP3PBOX 10.0
addions mol Na+ 0
addions mol Cl- 0
savepdb mol 4ZF6_solv.pdb
saveamberparm mol 4ZF6_solv.prmtop 4ZF6_solv.inpcrd
quit
 
